A submarine canyon led to the construction of the Hueneme Wharf in 1871 along the canyon by Thomas Bard. Until the construction of the Montalvo Cutoff that brought the railroad to nearby Oxnard, the wharf was the principal means of transportation for that portion of Ventura County lying south of the Santa Clara River. Hueneme was the second largest grain shippingport on the Pacific coast between 1871 and 1895.

Port Hueneme has a south-facing sand beach, known for its surfing. The beach stretches eastward about a mile from the harbor and the naval base and includes a wooden fishing pier. There are also picnic tables and barbecue grills.